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In May 2011 an increasing number of cases with gastroenteric symptoms were reported in German hospitals. The patients showed mainly an onset of vomiting and bloody diarrhoea. Because high numbers of these patients suffered from haemolytic uraemic syndrome (HUS), immediately HUS-inducing Shigatoxin-producing Escherichia coli were suspected of causing the outbreak. Shigatoxin-producing E. coli serotype O157:H7 is associated with HUS with a high prevalence worldwide, but also non-O157 serotypes are known to initiate HUS. Characterization of the responsible enteropathogenic E. coli identified it as a novel serotype, which possesses virulence factors combining those from enterohaemorrhagic E. coli and enteroaggregative E. coli. Hitherto available microbiological methods were unsuitable to accurately identify the outbreak. Rapid screening diagnostic methods were essential to ensure timely and appropriate patient management. This short review summarizes the molecular methods to detect E. coli O104:H4 and novel diarrhoeagenic E. coli strains appearing during the outbreak in Germany in 2011.